Diamond
Introduction
Diamond
is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:
Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.
Frameshift alignments for long read analysis.
Low resource requirements and suitable for running on standard desktops or laptops.
Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
Detailed about its usage can be found here: https://github.com/bbuchfink/diamond
Versions
2.0.13
2.0.14
2.0.15
2.1.6
Commands
diamond makedb
diamond prepdb
diamond blastp
diamond blastx
diamond view
diamond version
diamond dbinfo
diamond help
diamond test
Module
You can load the modules by:
module load biocontainers
module load diamond/2.0.14
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run diamond on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=diamond
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers diamond/2.0.14
diamond makedb --in uniprot_sprot.fasta -d uniprot_sprot
diamond blastp -p 24 -q test.faa -d uniprot_sprot --very-sensitive -o blastp_output.txt